Armillaria root rot (ARR) caused by Desarmillaria caespitosa and Armillaria mellea represents the main cause of premature stone fruit and nut tree decline in the United States. A. mellea is a primary concern for almond and peach growers in California, while D. caespitosa threatens peach production in the southeast region of the U.S. These fungi survive as facultative necrotrophs and colonize roots of several agriculturally important crops, including peach, almond, and sweet cherry. This colonization ultimately kills the woody roots and therefore host, severely limiting the tree’s lifespan and ability to provide a return on investment for the grower. Few management options are available to slow down ARR disease progression, and no management practice eliminates ARR fungi presence in an infested field. Additionally, most of the commercially available rootstocks are susceptible to infection, with only two peach/plum hybrid commercial rootstocks (Prunus umbellata × P. persica ‘MP-29’ and P. cerasifera × P. persica ‘Krymsk® 86’) showing partial resistance to ARR. The shared plum genetic background in these hybrids, paired with the lack of ARR resistance observed in peach germplasm suggests the source of resistance originated from plum. In this work, induced genetic responses in one susceptible accession, P. persica ‘Guardian®’, and two resistant accessions, P. cerasifera ’14-4’ and ‘MP-29’, when infected with D. tabescens and A. mellea were analyzed. Additionally, expression of genes encoding effectors and cell wall degrading enzymes (CWDEs) were investigated in the ARR fungi while infecting the three hosts. The results of the infection assays revealed unique responses between each of the three hosts in their progression of disease symptoms over time and in their transcriptomes while under infection by the two ARR fungi. Analysis identified key hub genes expressed by the two resistant Prunus accessions involved in the sensing and enzymatic degradation of chitin and the upregulation of GSTs, oxidoreductases, and transcription factors. Investigation of the ARR fungi transcriptomes similarly identified host-dependent expression of fungal effectors and CWDEs responsible for degrading the cell wall components cellulose, hemicellulose and pectin. Comprehensive analyses considering transcriptomes produced by both the host and pathogen during the infection course provides a deeper understanding of the factors driving resistant and susceptible responses to ARR infection, and their effects on the infecting pathogen’s gene expression.
Eastern filbert blight (EFB) disease caused by the fungal pathogen Anisogramma anomala (Peck) E. Müller is a major threat to Oregon’s hazelnut (Corylus avellana) industry. The Oregon State University (OSU) hazelnut breeding program has used ‘Gasaway’ as a source of resistance in many releases. Cultivars with ‘Gasaway’ resistance mapped to linkage group 6 (LG6) including ‘Jefferson’ and ‘McDonald’ have been extensively planted throughout Oregon’s Willamette Valley over the past decade. However ,‘Jefferson’ and ‘McDonald’ have exhibited small cankers in commercial orchards under high disease pressure. In New Jersey, cultivars with ‘Gasaway’ resistance develop large cankers. Thus, there are concerns about the long-term durability of ‘Gasaway’ resistance and the sustainability of Oregon’s hazelnut industry. The disease is also a main limiting factor to commercial hazelnut production in the eastern USA. New sources of resistance would be interesting, and a few major resistance genes have been mapped to LG7. Four populations were developed for fine mapping the LG7 resistance region using the ‘Ratoli’ (from Spain) and OSU 1166.123 (from Sochi, Russia) resistance sources. SSRs narrowed the resistance region to < 20 cM, and recombinant individuals were identified using 4-5 SSR loci within the region. Recombinants were inoculated with Anisogramma anomala in the greenhouse and in the field, and disease was evaluated 18 months later. A set of 22 new SSR markers were developed from di- and tri-nucleotide repeats between the flanking markers in the ‘Jefferson’ genome (v4). SSR markers were characterized using a diversity panel of 50 hazelnut accessions. To develop KASP/PACE primers for SNPs in the region, an initial set of 3000 SNPs was reduced to 100 using a SNP array. High density genetic linkage maps with new SSR and KASP markers were constructed for all four mapping populations. The results of this study will aid marker-assisted selection and the breeding of EFB-resistant cultivars with these new sources, and facilitate the pyramiding of R-genes in a single clonal selection for more durable resistance.
Improving nut and kernel quality traits is a high priority in almond breeding programs around the world. Almond has a long juvenile period and phenotypic selection for nut and kernel traits can only be conducted after three years from planting. In early stages of planting, individuals with desirable nut and kernel traits can be identified by marker-trait associations (MTAs) using molecular markers. Currently, MTAs are identified by quantitative trait locus (QTL) mapping using progeny from bi-parental crosses or association mapping panels. However, the efforts of identifying MTAs using current QTL detection methods are hampered either by unavailability of genomic information or required genetic linkage maps. In addition, most kernel traits have polygenic inheritance, and many genes and genomic regions affect genetic variations. In crop research, genomic selection would provide promising approach to accelerate the genetic gains and reduce the length of breeding cycle. Yet, application of genomic selection in almond breeding and research is limited. We present results demonstrating the predictive ability of whole-genome and pedigree-based models to identify elite candidate parents for almond kernel weight. In this work, we used ancestral pedigree and phenotypic data from 13,000 progeny that were derived from 57 parents and 291 families. Ancestral pedigrees were recorded from the available literature from the almond breeding programs in USA, Spain, Italy, France, and Australia. Average kernel weight was obtained for each progeny tree from 30 nuts. All parents were resequenced using whole-genome sequencing at a depth of 15x. Over 80k high quality, independent single-nucleotide polymorphisms were used to construct realised genomic relationship matrix and linkage disequilibrium (LD) regions were used to compute LD weights. Genomic best linear unbiased prediction (GBULP) using Asreml-R was used to predict genomic estimated breeding values (GEBV). Pedigree model derived from linear mixed model was used to predict individual tree effects (PEBV) to validate the predicted GEBVs. EBVs were compared using Pearson correlation coefficient (r) and elite candidate parents were selected based on the selection index. For kernel weight, both pedigree and genomic models resulted similar EBVs, and r was 0.97. A high level of correlation in EBVs obtained from two methods indicates the suitability of these models in estimating BVs for future predictions. Predicted elite candidate parents from this study can reduce the conventional breeding cycle of almond by 6 years. The constructed models mainly represent Australian context and multi-environmental trials are required to identify the broader applicability of these models.
Pecan (Carya illinoinensis), a North American native nut crop, exhibits two distinct flowering habits where male and female flowering occur at separate times. Trees that shed pollen before their pistillate flowers become receptive are classified as protandrous or type 1 (recessive homozygous, pp), while those with pistillate flowers receptive before pollen shed are protogynous or type 2 (dominant heterozygous, PP/Pp). Establishing commercial pecan orchards requires planting both types of pecan cultivars to ensure optimal pollination for maximum production. To investigate critical genes associated with pecan heterodichogamous flowering, we collected tissues from four stages (dormant buds, swollen buds, immature catkins, and immature pistils) of three genotypes (PP, Pp, and pp). Paired-end RNA sequencing at 125/150 bp read lengths was conducted on an Illumina platform. Clean and unique reads were mapped to an annotated 'Pawnee’ reference genome. Out of 32,267 annotated genes, over 5,000 (~15%) were identified to have alternative splicing events associated with pecan flowering dichogamy. We illustrate by three genes that present significant alternative splicing patterns associated with dichogamy genotypes, distinguishing the pp genotype from PP and Pp genotypes. These genes exhibited 6-18 nucleotide differences in RNA sequence between the pp genotype and PP/Pp genotypes, potentially resulting in an altered protein product with 2-6 amino acid differences between type 1 and type 2 genotypes. This study provides evidence for the prevalence of alternative RNA splicing in the transcription regulation of pecan dichogamy.
Specialty crop producers in Alaska need consistent, suitable crop and varietal options for successful commercial production, as food security is a major concern in this state that imports 95% of its food. The climate in much of Alaska is ideal for cool season, perennial corps that are winter hardy, such as Rhubarb (Rheum sp.). Rhubarb was brought to Alaska through several waves of immigration from regions extending from Russia through England and is now established throughout the state. Once a site for the National Plant Germplasm System (NPGS) Arctic and Subarctic Plant Gene Bank, the University of Alaska Fairbanks Matanuska Experiment Farm and Extension Center still maintains a collection of 41 accessions of Rheum sp. in the field. In addition, a new collection of heirloom rhubarb plants has been assembled by a local grower and maintained in large pots. In this project, we collected leaf samples from the heirloom collection plants for genotyping and phenotyping, as well as benchmark samples from plants remaining in the former germplasm collection, to provide an understanding of relatedness and desirable characteristics. A 5 cm square sample of leaf tissue was harvest from each plant, dried, and sent to a commercial laboratory for genotyping. Size and color of leaves and petioles, dates of emergence, plant vigor, and juice quality were measured on plants from the heirloom collection. Finally, surveys carried out of the last 12 years targeted a diversity of stakeholders (commercial producers, business owners, and the general public) to identify rhubarb quality expectations, including flavor, juice content, petiole color, and plant vigor. Based on genotyping results, plants not genetically redundant to those in the NPGS rhubarb collection currently located in Pullman, Washington, will be added to the collection. We present recommendations for variety suitability for different climate regions of Alaska based on the traits measured, taking into account varieties of rhubarb currently available wholesale to Alaska. Recommendations are also presented for further research into commercial production and added-value characteristics.
Horseradish (Armoracia rusticana, Brassicaceae) is an important specialty crop in Illinois, with most commercial production adjacent to St. Louis, Missouri in what is known as the Mississippi Bottoms. The continued development of new, improved horseradish cultivars is critical to sustain this important specialty crop industry, since horseradish clonal cultivars tend to "run out" and lose their productivity over a period of about 10 years. A small germplasm collection of clones from eastern Europe and Russia, as well as old cultivars no longer in wide use and other breeding materials that were saved from the breeding program has been maintained since the 1960s, first at University of Illinois until the early 2000s and now at Southern Illinois University-Carbondale. During the last 20 years, germplasm has been utilized from various sources to improve horseradish so this industry can sustain itself for the near future. The following examples are provided to illustrate the importance of new germplasm in new horseradish cultivar development. Accession 761A collected from Drążgów, Poland was instrumental in developing horseradish cultivars with tolerance to internal root discoloration which is caused by a soil-borne pathogen complex. The germplasm clone Czech has been very effective in transmitting its large root size trait to its resulting progeny and was used in many crosses made from 2005 to 2010. Many cultivars grown today have this germplasm source in their background. Another important clonal cultivar known as 9705 was widely grown during the 2000s and resulted from outcrossing accession 758A collected from Ribnica, Slovenia with an unknown male. Additionally, 315 is another very important cultivar that was the workhorse for the industry from 2005 to 2015 having lineage also from 758A. 15K was another industry workhorse in the late 1990s to early 2000s, and had its primary lineage traceable to 856A, an accession from the Czech Republic. These are a few examples of how germplasm sources have contributed to sustaining the Illinois horseradish industry and each will be discussed in further detail regarding their specific benefits. Moreover, most are still used in some capacity in the breeding program today.
